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Lei S, Chen L, Liang F, Zhang Y, Zhang C, Xiao H, Tang R, Yang B, Wang L, Jiang H. Identification of a major QTL and candidate genes analysis for branch angle in rapeseed ( Brassica napus L.) using QTL-seq and RNA-seq. FRONTIERS IN PLANT SCIENCE 2024; 15:1340892. [PMID: 38450405 PMCID: PMC10914954 DOI: 10.3389/fpls.2024.1340892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024]
Abstract
Introduction Branching angle is an essential trait in determining the planting density of rapeseed (Brassica napus L.) and hence the yield per unit area. However, the mechanism of branching angle formation in rapeseed is not well understood. Methods In this study, two rapeseed germplasm with extreme branching angles were used to construct an F2 segregating population; then bulked segregant analysis sequencing (BSA-seq) and quantitative trait loci (QTL) mapping were utilized to localize branching anglerelated loci and combined with transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qPCR) for candidate gene mining. Results and discussion A branching angle-associated quantitative trait loci (QTL) was mapped on chromosome C3 (C3: 1.54-2.65 Mb) by combining BSA-seq as well as traditional QTL mapping. A total of 54 genes had SNP/Indel variants within the QTL interval were identified. Further, RNA-seq of the two parents revealed that 12 of the 54 genes were differentially expressed between the two parents. Finally, we further validated the differentially expressed genes using qPCR and found that six of them presented consistent differential expression in all small branching angle samples and large branching angles, and thus were considered as candidate genes related to branching angles in rapeseed. Our results introduce new candidate genes for the regulation of branching angle formation in rapeseed, and provide an important reference for the subsequent exploration of its formation mechanism.
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Affiliation(s)
- Shaolin Lei
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Li Chen
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Fenghao Liang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuling Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Chao Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Huagui Xiao
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rong Tang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Bin Yang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Lulu Wang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Huanhuan Jiang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
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Hu XG, Zhuang H, Lin E, Borah P, Du M, Gao S, Wang T, Tong Z, Huang H. Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight Into Molecular Mechanisms of Cellulose and Lignin Biosynthesis in Cunninghamia lanceolata. FRONTIERS IN PLANT SCIENCE 2022; 13:883720. [PMID: 35712576 PMCID: PMC9194830 DOI: 10.3389/fpls.2022.883720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/06/2022] [Indexed: 05/31/2023]
Abstract
Cunninghamia lanceolata is an essential timber species that provide 20%-30% raw materials for China's timber industry. Although a few transcriptomes have been published in C. lanceolata, full-length mRNA transcripts and regulatory mechanisms behind the cellulose and lignin biosynthesis have not been thoroughly investigated. Here, PacBio Iso-seq and RNA-seq analyses were adapted to identify the full-length and differentially expressed transcripts along a developmental gradient from apex to base of C. lanceolata shoots. A total of 48,846 high-quality full-length transcripts were obtained, of which 88.0% are completed transcriptome based on benchmarking universal single-copy orthologs (BUSCO) assessment. Along stem developmental gradient, 18,714 differentially expressed genes (DEGs) were detected. Further, 28 and 125 DEGs were identified as enzyme-coding genes of cellulose and lignin biosynthesis, respectively. Moreover, 57 transcription factors (TFs), including MYB and NAC, were identified to be involved in the regulatory network of cellulose and lignin biosynthesis through weighted gene co-expression network analysis (WGCNA). These TFs are composed of a comparable regulatory network of secondary cell wall formation in angiosperms, revealing a similar mechanism may exist in gymnosperms. Further, through qRT-PCR, we also investigated eight specific TFs involved in compression wood formation. Our findings provide a comprehensive and valuable source for molecular genetics breeding of C. lanceolata and will be beneficial for molecular-assisted selection.
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Affiliation(s)
- Xian-Ge Hu
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Hebi Zhuang
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Erpei Lin
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Priyanka Borah
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Mingqiu Du
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Shiya Gao
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Tongli Wang
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Zaikang Tong
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Huahong Huang
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Zhang W, Ma J, Yan Q, Jiang Z, Yang S. Biochemical characterization of a novel acidic chitinase with antifungal activity from Paenibacillus xylanexedens Z2-4. Int J Biol Macromol 2021; 182:1528-1536. [PMID: 34022308 DOI: 10.1016/j.ijbiomac.2021.05.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/21/2021] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
A chitinase gene (PxChi52) from Paenibacillus xylanexedens Z2-4 was cloned and heterologously expressed in Escherichia coli BL21 (DE3). PxChi52 shared the highest identity of 91% with a glycoside hydrolase family 18 chitinase (ChiD) from Bacillus circulans. The recombinant enzyme (PxChi52) was purified and biochemically characterized. PxChi52 had a molecular mass of 52.8 kDa. It was most active at pH 4.5 and 65 °C, respectively, and stable in a wide pH range of 4.0-13.0 and up to 50 °C. The enzyme exhibited the highest specific activity of 16.0 U/mg towards colloidal chitin, followed by ethylene glycol chitin (5.4 U/mg) and ball milled chitin (0.4 U/mg). The Km and Vmax values of PxChi52 towards colloidal chitin were determined to be 3.06 mg/mL and 71.38 U/mg, respectively, PxChi52 hydrolyzed colloidal chitin and chitooligosaccharides with degree of polymerization 2-5 to release mainly N-acetyl chitobiose. In addition, PxChi52 displayed inhibition effects on the growth of some phytopathogenic fungi, including Alternaria alstroemeriae, Botrytis cinerea, Rhizoctonia solani, Sclerotinia sclerotiorum and Valsa mali. The unique properties of PxChi52 may enable it potential application in agriculture field as a biocontrol agent.
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Affiliation(s)
- Wenjiao Zhang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Junwen Ma
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Qiaojuan Yan
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Zhengqiang Jiang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Shaoqing Yang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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